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- PDB-1myl: SUBSTITUTING HYDROPHOBIC RESIDUES FOR A BURIED SALT BRIDGE ENHANC... -

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Basic information

Entry
Database: PDB / ID: 1myl
TitleSUBSTITUTING HYDROPHOBIC RESIDUES FOR A BURIED SALT BRIDGE ENHANCES PROTEIN STABILITY BUT DOES NOT REDUCE CONFORMATIONAL SPECIFICITY
ComponentsARC REPRESSOR
KeywordsTRANSCRIPTION REGULATION / HYPERSTABLE MUTANT
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Arc-like DNA binding domain / Arc-like DNA binding domain / Met repressor-like / Arc Repressor Mutant / Arc-type ribbon-helix-helix / Ribbon-helix-helix / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcriptional repressor arc
Similarity search - Component
Biological speciesEnterobacteria phage P22 (virus)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsSchildbach, J.F. / Waldburger, C.D. / Sauer, R.T.
Citation
Journal: Nat.Struct.Biol. / Year: 1995
Title: Are buried salt bridges important for protein stability and conformational specificity?
Authors: Waldburger, C.D. / Schildbach, J.F. / Sauer, R.T.
#1: Journal: Nature / Year: 1994
Title: DNA Recognition by Beta-Sheets in the Arc Repressor-Operator Crystal Structure
Authors: Raumann, B.E. / Rould, M.A. / Pabo, C.O. / Sauer, R.T.
History
DepositionOct 6, 1994Processing site: BNL
Revision 1.0Jan 26, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ARC REPRESSOR
B: ARC REPRESSOR
C: ARC REPRESSOR
D: ARC REPRESSOR
E: ARC REPRESSOR
F: ARC REPRESSOR


Theoretical massNumber of molelcules
Total (without water)37,2146
Polymers37,2146
Non-polymers00
Water63135
1
A: ARC REPRESSOR
B: ARC REPRESSOR


Theoretical massNumber of molelcules
Total (without water)12,4052
Polymers12,4052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-24 kcal/mol
Surface area5390 Å2
MethodPISA
2
E: ARC REPRESSOR
F: ARC REPRESSOR


Theoretical massNumber of molelcules
Total (without water)12,4052
Polymers12,4052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-22 kcal/mol
Surface area5220 Å2
MethodPISA
3
C: ARC REPRESSOR
D: ARC REPRESSOR


Theoretical massNumber of molelcules
Total (without water)12,4052
Polymers12,4052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-22 kcal/mol
Surface area5350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.600, 117.100, 49.700
Angle α, β, γ (deg.)90.00, 98.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
ARC REPRESSOR


Mass: 6202.298 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage P22 (virus) / Genus: P22-like viruses / Gene: MUTATED ARC GENE / Plasmid: PSA300-MYL GENE: MUTATED ARC GENE / Production host: Escherichia coli (E. coli) / References: UniProt: P03050
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.24 %
Crystal
*PLUS
Density % sol: 49.5 %
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein11
230 mMbis-Tris-propane-Cl11
31 mM11NaN3
419-22 %PEG340012
5100 mMTris-HCl12
6200 mMNa-acetate12

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 11168 / % possible obs: 90.8 % / Observed criterion σ(I): 0
Reflection
*PLUS
Highest resolution: 2.4 Å / Num. measured all: 20111 / Rmerge(I) obs: 0.062

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.4→6 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.293 --
Rwork0.209 --
obs0.209 11168 90.8 %
Displacement parametersBiso mean: 33.2 Å2
Refinement stepCycle: LAST / Resolution: 2.4→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2140 0 0 35 2175
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.55
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d19.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.31
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.131.1
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it3.712
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.209 / Rfactor Rfree: 0.293
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 1.55

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